I don't think you were pushing to the devel builders correctly. The last
commit we have on the builder is Sat Feb 29th.
commit b810b6a81198438d6ad26b7d86b14eece00dfa59
Author: lrutter <lindsayannerut...@gmail.com>
Date: Sat Feb 29 23:44:08 2020 +0900
Fix version issue
So you never actually pushed the changes to the git.biocnductor upstream
server.
Based on what you have below please do the following and if you have any ERRORs
please paste the command with the output so we can better assist you.
git fetch --all
git pull upstream master
# make sure your version number is 1.3.2
# I'm not sure if the version number higher in the history will cause problems.
If you get an error about version number I suggest then doing 1.3.6
# which is one higher than it looks like
git push upstream master
The upstream in these commands says to pull/push to the upstream remote which
is pointed at the bioconductor git servers.
The master says to pull/push from the master branch of the given repository.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: L Rutter <lindsayannerut...@gmail.com>
Sent: Tuesday, March 10, 2020 4:11 AM
To: Shepherd, Lori <lori.sheph...@roswellpark.org>
Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
Dear Lori:
Thank you very much for your very helpful response. I am sorry to say that I
still am having difficulty seeing errors I think I resolved locally get
successfully pushed to my devel branch. I would really appreciate your feedback
to help me possibly identify the problem.
First, I checked that my git remotes are set up correctly. Below is my output:
origin https://github.com/lindsayrutter/bigPint.git (fetch)
origin https://github.com/lindsayrutter/bigPint.git (push)
upstream g...@git.bioconductor.org:packages/bigPint.git (fetch)
upstream g...@git.bioconductor.org:packages/bigPint.git (push)
In an attempt to push changes to my devel branch, I updated my DESCRIPTION file
to contain version 1.3.2. My last commit can be seen
here<https://github.com/lindsayrutter/bigPint/commit/1f61951168d5ba35be6464c3f082e006ff2dd220>.
I waited a few days and see that my
builder<http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/malbec2-checksrc.html>
is still failing. The ERROR seems to be coming from my R/convertSEPair.R
script in the line:
vapply(colnames(oldData), function(x) strsplit(x, "[.]")[[1]][1])
I had updated this command, changing “vapply” to
“lapply”. It now reads:
lapply(colnames(oldData), function(x) strsplit(x, "[.]")[[1]][1])
I double-checked the R/convertSEPair.R file on my latest GitHub
commit<https://github.com/lindsayrutter/bigPint/blob/1f61951168d5ba35be6464c3f082e006ff2dd220/R/convertSEPair.R>
and indeed the “vapply” command is no longer present.
I also note that my “Last commit” field on the builder
website<http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/malbec2-checksrc.html>
is b810b6a from February 29, whereas my latest intended GitHub commit for the
devel branch was 1f61951 from March 8.
I should also state that I had tried a few times and kept bumping up my version
number. So, on March 7 (Commit c75da1e), I had version 1.3.5. In my latest
commit, I reduced my version number to 1.3.2 just to check that the reason my
devel branch was still failing was not simply because my z (x.y.z) number was
increased by more than a value of 1. However, it seems my pushed changes on
GitHub are not updating to the devel builder website.
I really thank you for sharing your advice with me. I wanted to ask if you may
have any ideas on what I may be missing at this stage. Thank you again for your
support.
Sincerely,
Lindsay
2020年3月3日(火) 21:30 Shepherd, Lori
<lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>:
It can take up to 24 from a push to be reflected on the build report.
For release 3.10 (RELEASE_3_10 branch) we see a version number of 1.2.0
http://bioconductor.org/checkResults/release/bioc-LATEST/bigPint/
and
For devel 3.11 (master branch) we see a version number of 1.3.1 as well
http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/
The landing page http://bioconductor.org/packages/3.11/bioc/html/bigPint.html
will only be updated on a successful build/check of the package so we don't
propagate broken packages to users. If the fixes did not allow for a clean
build and check it would not be reflected.
Also remember that in order for a change to propagate you need a valid version
bump. So your release version 1.2.0 in order to take effect would have needed
to be 1.2.1. And for devel master branch you would need a version of 1.3.2.
Never apologize for asking questions. We are here to help. And we appreciate
that you are taking the time to fix the package and learn how to push the
changes up correct.
I'll answer your specific questions below:
Firstly make sure your git remotes are set up correctly where origin is your
github repository and upstream is pointing to the bioconductor repositories
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
origin (your github)
origin (your github)
upstream g...@git.bioconductor.org:packages/bigPint.git (fetch)
upstream g...@git.bioconductor.org:packages/bigPint.git (push)
1) Is it acceptable for me to push what is on my GitHub master branch (1.3.1)
to the development branch of Bioconductor?
Yes. however you will want to bump the version number in the DESCRIPTION to
1.3.2 because we have version 1.3.1 on our builders as indicated
http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/. This page
reflects 1.3.0 because 1.3.1 has not built without ERROR and we would not
propagate broken packages to users
http://bioconductor.org/packages/3.11/bioc/html/bigPint.html.
2) Is it acceptable for me to likewise push what is on my GitHub master branch
(1.3.1) to the release branch of Bioconductor? I am assuming I am only supposed
to push the "cherry-pick" commits that resolve what had been causing an error
originally? This may be difficult for me as I have since added many more
changes to the master branch on GitHub after resolving that release error.
Yes although not recommended but we would rather have a working package than
one ERRORing so if you don't think you can cherry-pick than yes. The best
option for that would be to checkout the RELEASE_3_10 branch and do a git
merge master. You will have to change the version number in the DESCRIPTION to
be consistent with release version numbers. (1.2.1) AFTER the merge.
3) Is it possible to ask if there is anything else identifiably "out of line"
with my setup (on my GitHub master, development branch, or release branch)? I
am sure that once I complete this process successfully I will have be better
positioned to critically think of what is happening - but right now I worry
that due to my earlier mistakes, something may be "off" with my setup that will
make it difficult for me to successfully follow any set of instructions.
I think you were on the right track so no further comments.
Some helpful hints :
1. git fetch --all will fetch all branches from your origin github and the
upstream bioconductor location (this will be important to do after the next
release in april to get the next RELEASE_3_11 branch)
2. it is always a good idea to do a git pull upstream (branch name) to
pull any changes we have made. occasionally if we made an infrastructure change
bioconductor will apply patches. We also do the version bump changes at
release time. So for your master devel branch git pull upstream master (git
pull upstream RELEASE_3_10 for the current release)
3. If you do git merge read the out message carefully and make sure there
are no conflicts. Conflicts means there is code that was changes in both files
(locally and on the branch you want to merge) so you will have to check the
file to make sure you don't include merge conflicts - The code conflicts are
indicated with >>>>> and <<<<<. you delete those and keep the changes
you want to commit. Then add and commit like normal and git should give you
messages about resolving conflicts.
Hope this helps. Let me know if you run into any further trouble.
Cheers
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: L Rutter <lindsayannerut...@gmail.com<mailto:lindsayannerut...@gmail.com>>
Sent: Tuesday, March 3, 2020 5:55 AM
To: Shepherd, Lori <lori.sheph...@roswellpark.org>
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
<bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
Dear Lori:
Thank you for this helpful advice. I did successfully now manage to change my
keys and name on the git.credentials app you suggested on February 25.
At that time, my development version was building but my release version was
failing. So, I followed the instructions in the link you provided on February 3
(http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/)
to update my release version. I was able to also follow the "Sync existing
repositories" tab at the beginning of the guideline.
After waiting for the updates, when I checked into my package (bigPint), I
noticed now both the development
(https://bioconductor.org/packages/devel/bioc/html/bigPint.html) and release
(https://bioconductor.org/packages/release/bioc/html/bigPint.html) version are
not building. I was surprised because I did not think I was making any changes
to the development version through these instructions. I also notice my
development version is 1.3.0, my release version is 1.2.0, and my GitHub master
branch (https://github.com/lindsayrutter/bigPint/blob/master/DESCRIPTION) is
version 1.3.1. It also seems that the version on my local computer reversed to
1.2.0.
I tentatively plan to:
1) Clone my GitHub master branch (version 1.3.1) back to my local computer (to
make sure I do not lose many recent changes I have made to my package).
2) Try to push my most current version (1.3.1) to the development branch of
Bioconductor.
3) Try to push changes to the release branch of Bioconductor.
I am pretty stuck even to the point where it is hard for me to formulate
questions but below are a few questions that might help me identify the point
of confusion:
1) Is it acceptable for me to push what is on my GitHub master branch (1.3.1)
to the development branch of Bioconductor?
2) Is it acceptable for me to likewise push what is on my GitHub master branch
(1.3.1) to the release branch of Bioconductor? I am assuming I am only supposed
to push the "cherry-pick" commits that resolve what had been causing an error
originally? This may be difficult for me as I have since added many more
changes to the master branch on GitHub after resolving that release error.
3) Is it possible to ask if there is anything else identifiably "out of line"
with my setup (on my GitHub master, development branch, or release branch)? I
am sure that once I complete this process successfully I will have be better
positioned to critically think of what is happening - but right now I worry
that due to my earlier mistakes, something may be "off" with my setup that will
make it difficult for me to successfully follow any set of instructions.
I apologize for reaching out about this headache of an issue now. I am just
concerned I may not be able to resolve this in a timely manner with my current
scope of knowledge.
Sincerely,
Lindsay
2020年2月25日(火) 21:14 Shepherd, Lori
<lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>:
Thank you for reaching out. Have you tried checking your keys and changing
your name on the git.credentials app?
https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: L Rutter <lindsayannerut...@gmail.com<mailto:lindsayannerut...@gmail.com>>
Sent: Tuesday, February 25, 2020 1:55 AM
To: Shepherd, Lori <lori.sheph...@roswellpark.org>
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
<bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
Dear Lori:
Thanks for the suggestions. I tried to follow the linked instructions on
February 4 and February 9, but was unsuccessful both times (i.e. did not see
the changes pushed to the release branch). I tried following the instructions
again today. I notice that when I issue the command:
git merge upstream/master
I receive the message:
merge: upstream/master - not something we can merge
So, I clicked on the "Sync existing repositories" tab and checked that the
instructions there were working. After adding the upstream branch as follows:
git remote add upstream g...@git.bioconductor.org:packages/bigPint.git
When I then try to fetch all (git fetch --all), I receive the following error:
Fetching origin
Fetching upstream
FATAL: R any packages/bigpint lrutter DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream
I changed my GitHub userName about one year ago from "lrutter" to
"lindsayrutter". By doing "git remote -v", I can see that my origin branches
are correctly at "lindsayrutter", but I am unable to see about my upstream
branches on git.bioconductor. This is my output from "git remote -v":
origin https://github.com/lindsayrutter/bigPint (fetch)
origin https://github.com/lindsayrutter/bigPint (push)
upstream g...@git.bioconductor.org:packages/bigpint.git (fetch)
upstream g...@git.bioconductor.org:packages/bigpint.git (push)
Do you have any advice on how I can fix this issue with fetch upstream possibly
expecting my older userName? Thank you for sharing advice.
Sincerely,
Lindsay
2020年2月3日(月) 21:54 Shepherd, Lori
<lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>:
It looks like you only pushed changes to the master branch which is our devel
branch (3.11).
Please see the instructions for
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
where RELEASE_X_Y would be RELEASE_3_10 for pushing changes to the release
3.10 branch.
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel
<bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on
behalf of L Rutter
<lindsayannerut...@gmail.com<mailto:lindsayannerut...@gmail.com>>
Sent: Saturday, February 1, 2020 4:18 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
<bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
Dear all:
I have been receiving messages that my Bionconductor package bigPint is
producing errors on 'R CMD build' on malbec1. I believe I discovered the
source of the error, fixed it, and pushed changes to my GitHub account (
github.com/lindsayrutter<http://github.com/lindsayrutter>) on December 10,
2019. I continued to receive this
error notification and was advised to ensure I had pushed the changes to
Bioconductor. I pushed changes following these instructions (
http://bioconductor.org/developers/how-to/git/) on January 4, 2020. I am
still receiving notifications that my package produces errors on 'R CMD
build' on malbec1 (
https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/bigPint/malbec1-buildsrc.html).
However, it seems my package is no longer failing daily build reports for
version 3.11 as of January 4, 2020 (
http://bioconductor.org/checkResults/3.11/bioc-LATEST/).
I am seeking advice on what a maintainer should try in this situation? Is
it possible my changes were only recognized in version 3.11 but not version
3.10? Thank you for any advice you may have!
Sincerely,
L. Rutter
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